Comprehensive profiling of SARS-CoV-2 antibody responses and escape pathways

SARS-CoV-2 抗体反应和逃逸途径的综合分析

• 批准号: 10398436
• 负责人: JULIE M. OVERBAUGH
• 金额: $ 12.34万
• 依托单位: FRED HUTCHINSON CANCER CENTER
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-01 至 2024-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10398436
• 关键词: 2019-nCoV; Amino Acid Sequence; Amino Acids; Antibodies; Antibody Response; Antiviral Agents; Bacteriophages; Binding; Biological Assay; C-terminal; COVID-19; Cell fusion; Cells; Chimeric Proteins; Clinical; Complement; Coronavirus; Coronavirus Infections; Coronavirus spike protein; Cryoelectron Microscopy; Data; Development; Diagnostic; Disease; Ebola virus; Epitopes; Exhibits; Genetic; Genome; Goals; HIV; HIV Antibodies; Immune; Immunoprecipitation; Infection; Kinetics; Libraries; Methods; Middle East Respiratory Syndrome; Molecular Conformation; Monoclonal Antibodies; Mutation; N-terminal; Outcome; Pathogenesis; Pathway interactions; Peptide Hydrolases; Peptide Library; Peptides; Phage Display; Pharmaceutical Preparations; Plasma; Population; Preventive treatment; Process; Proteins; Resolution; Role; SARS coronavirus; SARS-CoV-2 infection; Sampling; Source; Structure; Therapeutic; Therapeutic antibodies; Vaccine Design; Vaccines; Variant; Viral; Viral Proteins; Virus; Work; conformational conversion; convalescent plasma; cross reactivity; deep sequencing; design; drug candidate; flexibility; mutation screening; neutralizing antibody; novel; pandemic disease; protein aminoacid sequence; rapid technique; receptor; receptor binding; response; vaccine candidate; vaccine-induced antibodies

The ongoing global pandemic of the novel SARS-CoV-2 coronavirus (CoV) presents an urgent need for development of effective preventative and treatment therapies. The viral-host cell fusion (S) protein spike is a prime target for such therapies owing to its critical role in the virus lifecycle. The S protein is divided into two regions: the N-terminal S1 domain that caps the C-terminal S2 fusion domain. Binding to host receptor via the Receptor Binding Domain (RBD) in S1 is followed by proteolytic cleavage of the spike by host proteases. This leads dramatic conformational transitions resulting in S1 shedding and exposure of the fusion machinery in S2, culminating in host-cell entry. Class I fusion proteins such as the CoV S protein that undergo large conformational changes during the fusion process must, by necessity, be highly flexible and dynamic. Indeed, cryo-EM structures of the SARS-CoV-2 spike reveal considerable flexibility and dynamics in the S1 domain, especially around the RBD that exhibits two discrete conformational states – a “down” state that is shielded from receptor binding, and an “up” state that is receptor-accessible. The overall goals of this study are to use our robust, high-throughput computational and experimental pipeline to define the detailed trajectory of the “down” to “up” transition of the SARS-CoV-2 S protein, identify early metastable intermediates in the fusion pathway, and exploit their structures and dynamics for identifying drug and vaccine candidates that target SARS-CoV-2. A wealth of structural information on CoV spike proteins, including recently determined cryo-EM structures of the SARS-CoV-2 spike, provides a rich source of detailed data from which to begin precise examination of macromolecular transitions underlying triggering of this fusion machine. The scientific premise of this study is that understanding the structural dynamics and early transition kinetics of mobile regions of the SARS-CoV-2 spike will allow optimal control of vaccine and drug responses, and facilitate the development of novel antiviral drugs and protective vaccines. At the culmination of this study, we expect to have determined structures of multiple “down”, “up”, and intermediate states of the SARS-CoV-2 S protein. Together, these studies will provide important atomically detailed structural and mechanistic information for exploitation in vaccine and therapeutics design.

新型SARS-COV-2冠状病毒（COV）持续的全球大流行表明，迫切需要开发有效的预防和治疗疗法。病毒宿主细胞融合（S）蛋白峰值是由于其在病毒生命周期中的关键作用而成为此类疗法的主要靶标。 S蛋白分为两个区域：限制C末端S2融合结构域的N端S1结构域。通过S1中的受体结合结构域（RBD）与宿主受体结合，然后通过宿主蛋白酶对峰值进行蛋白水解裂解。这导致了戏剧性的会议转变，导致S1脱落和融合机械在S2中的曝光，最终导致宿主细胞进入。 I类融合蛋白，例如在融合过程中经历大构象变化的COV蛋白必须高度柔韧性和动态性。实际上，SARS-COV-2尖峰的冷冻EM结构显示了S1结构域中的相当大的灵活性和动力学，尤其是在RBD周围表现出两个离散构象状态 - 这种“向下”状态，它被屏蔽了受体结合，以及一种“ UP”状态，可接近受体。这项研究的总体目标是使用我们的强大，高通量计算和实验管道来定义 SARS-COV-2 S蛋白的“向上”过渡，识别融合途径中的早期亚稳态中间体，并利用其结构和动力学来识别靶向SARS-COV-2的药物和疫苗候选者。有关COV SPIKE蛋白的大量结构信息，包括最近确定的SARS-COV-2 SPIKE的冷冻EM结构，提供了丰富的详细数据来源，从中可以从中开始对这款融合机的基础触发的大分子过渡的精确检查。这项研究的科学前提是，了解SARS-COV-2 SPIKE的移动区域的结构动力学和早期过渡动力学将允许对疫苗和药物反应的最佳控制，并支持新型抗病毒药物的发展和受保护的疫苗。在这项研究的顶点下，我们希望已经确定了SARS-COV-2 S蛋白的多个“下降”，“向上”和中间状态的结构。总之，这些研究将为疫苗和治疗中的剥削提供重要的原子质结构和机械信息。

项目成果

Distinct Antibody Responses to Endemic Coronaviruses Pre- and Post-SARS-CoV-2 Infection in Kenyan Infants and Mothers.

• DOI: 10.3390/v14071517
• 发表时间: 2022-07-12
• 期刊: Viruses

High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies.

• DOI: 10.1016/j.cell.2021.04.045
• 发表时间: 2021-05-27
• 期刊: Cell
• 影响因子: 64.5
• 作者: Garrett ME;Galloway J;Chu HY;Itell HL;Stoddard CI;Wolf CR;Logue JK;McDonald D;Weight H;Matsen FA 4th;Overbaugh J
• 通讯作者: Overbaugh J

Comparison of nucleocapsid and spike antibody ELISAs for determining SARS-CoV-2 seropositivity in Kenyan women and infants.

• DOI: 10.1002/jmv.28221
• 发表时间: 2023-01
• 期刊: JOURNAL OF MEDICAL VIROLOGY
• 影响因子: 12.7
• 作者: Fish, Carolyn S.;Owiti, Prestone;Begnel, Emily R.;Itell, Hannah L.;Ojee, Ednah;Adhiambo, Judith;Ogweno, Vincent;Holland, LaRinda A.;Richardson, Barbra A.;Khan, Adam K.;Maqsood, Rabia;Gantt, Soren;Lim, Efrem S.;Slyker, Jennifer;Kinuthia, John;Overbaugh, Julie;Wamalwa, Dalton;Lehman, Dara A.;Chohan, Bhavna H.
• 通讯作者: Chohan, Bhavna H.

Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection.

对 SARS-CoV-2 Spike 蛋白的抗体反应的全面表征发现，除了轻度感染的表位之外，还有其他疫苗诱导的表位。

• DOI: 10.7554/elife.73490
• 发表时间: 2022-01-24
• 期刊: eLife
• 影响因子: 7.7
• 作者: Garrett ME;Galloway JG;Wolf C;Logue JK;Franko N;Chu HY;Matsen FA 4th;Overbaugh JM
• 通讯作者: Overbaugh JM

SARS-CoV-2 Antibody Binding and Neutralization in Dried Blood Spot Eluates and Paired Plasma.

• DOI: 10.1128/spectrum.01298-21
• 发表时间: 2021-10-31
• 期刊: Microbiology spectrum
• 影响因子: 3.7
• 作者: Itell HL;Weight H;Fish CS;Logue JK;Franko N;Wolf CR;McCulloch DJ;Galloway J;Matsen FA 4th;Chu HY;Overbaugh J
• 通讯作者: Overbaugh J